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<H2>Chemical Editor Concepts</H2>
<p>The structure editor is used to draw chemical molecules, substructure fragments,
reactions and simple drawing objects like text, boxes, etc. Its functionality changes
depending on the kind of object(s) being edited. Thus, the atom mapping tool is only available,
when a reaction is edited. Query feature dialogs only open, when a substructure is edited, etc.</p>
<br>
<H3>Atom and Bond Hot-Keys</H3>
<p>Hot-keys allow to quickly change atom and bond types or to attach common groups to an atom.
When the mouse is moved over an atom or bond then the atom or bond is automatically highlighted,
indicating that mouse clicks or pressing a hot-key affect the highlighted object.</p>
<p><table BORDER=1 CELLSPACING=0 CELLPADDING=4 CLASS=body width="100%"> <tr align="Left">  <th>Hot-Key</th>  <th>Type</th>  <th>Name</th>  <th>Explanation</th> </tr> <tr>
  <td><b>'Delete'</b></td>
  <td>Atoms<br>Bonds<br>Mapping</td>
  <td>Delete</td>
  <td>Deletes highlighted and selected atoms and bonds. When a reaction is edited and
the mapping tool is selected, then pressing the 'Delete' key removes all atom mapping from the reaction.
  </td>
 </tr>
 <tr>
  <td><b>'1','2','3', ...</b></td>
  <td>Atom</td>
  <td>Atom Chain</td>
  <td>Attaches a chain of 'n' carbon atoms to the highlighted atom provided that its valence maximum is not exceeded.</td>
 </tr>
 <tr>
  <td><b>'+', '-'</b></td>
  <td>Atom</td>
  <td>Charge Modifiers</td>
  <td>Increases or decreases the charge of the highlighted atom.</td>
 </tr>
 <tr>
  <td><b>'?'</b></td>
  <td>Atom</td>
  <td>Connection Point</td>
  <td>Converts an atom into a connection point of a substituent or building block.</td>
 </tr>
 <tr>
  <td><b>'q'</b></td>
  <td>Atom,<br>Bond</td>
  <td>Query Feature Dialog</td>
  <td>If a substructure query is edited then this key opens a query feature dialog,
which allows to specify additional atom/bond conditions for the substructure search.</td>
 </tr>
 <tr>
  <td><b>'1','2','3'</b></td>
  <td>Bond</td>
  <td>Bond Order</td>
  <td>Changes the highlighted bond into a single, double or triple bond.</td>
 </tr>
 <tr>
  <td><b>'u'</b></td>
  <td>Bond</td>
  <td>Up Bond</td>
  <td>Changes the highlighted bond into 'up' stereo bond, if at least one of the associated
atoms is a relative or absolute stereo center.</td>
 </tr>
 <tr>
  <td><b>'d'</b></td>
  <td>Bond</td>
  <td>Down Bond</td>
  <td>Changes the highlighted bond into 'down' stereo bond, if at least one of the associated
atoms is a relative or absolute stereo center.</td>
 </tr>
 <tr>
  <td><b>'c'</b></td>
  <td>Bond</td>
  <td>Cross Bond</td>
  <td>Changes the highlighted bond into a double bond with unknown configuration.</td>
 </tr>
 <tr>
  <td><b>'4','5','6','7'</b></td>
  <td>Bond</td>
  <td>Annelate Ring</td>
  <td>Annellates a new saturated ring with the respective ring size to the highlighted bond.</td>
 </tr>
 <tr>
  <td><b>'b'</b></td>
  <td>Bond</td>
  <td>Annelate Benzo</td>
  <td>Annellates a new benzene ring to the highlighted bond.</td>
 </tr>
</table></p>

<br>
<H3>Atom labels & Substituents & Protecting Groups</H3>
<p>If an atom is highlighted one may type multiple keys to define an atom label or common
group name. The key sequence is shown in the editor and in black, if it is a valid atom label.
It is shown in blue, if it is a recognized substituent or protecting group name. It is shown in
gray, if it can be completed to a known group name and it is shown in red, if no valid completion
is possible. After typing a valid atom symbol or group name and moving the mouse away or typing
<i>Enter</i> the atom is converted according to the atom label or a substituent is attached accoringly.
For the sake of convenience atom labels or group names can be typed in as lower case letters and dashes
in group names may be omitted. E.g. typing 'n' followed by 'a' converts the atom to a sodium atom
and typing 'otolyl' attaches an ortho-Tolyl group.</p>
<p>Known group names are: Ac, Alloc, Allyl, Am, Benzoyl, Benzyl, Boc, BOM, Bn, Bs, Bt, Btm, Bu, Bz,
Bzh, Bzl, BzOM, Cbz, Cy, cyclobutyl, cycloheptyl, cyclooctyl, cyclopentyl, cyclopropyl, Dan, DEAE, DEIPS,
DMIPS, DMPM, DMPS, DMTr, DNP, DNS, DPIPS, DPTBS, DTBMS, Et, Fmoc, i-Am, i-Bu, i-Pr, Im, m-Tolyl, MDIPS,
MDPS, MEM, MMTr, MOM, MPM, MTM, Me, Mes, Ms, N3, n-Am, n-Bu, n-Pr, neo-Am, nitro, NO2, Np, o-Tolyl, p-Tolyl,
PMB, PMBM, PNB, PPi, Ph, Phenyl, Pht, Piv, Poc, Pr, Pv, s-Am, s-Bu, s-Butyl, SEM, SES, t-Am, t-Bu, t-Butyl,
TBDMS, TBDPS, TBMPS, TBS, TDS, TFA, THF, THP, TIPS, TMS, Tf, Thexyl, Tos, Troc, Trt, Ts, Xyl.</p>

<br>
<H3>Buttons and Tools</H3>
<p>Chemical structures are drawn by selecting an appropriate tool and applying it
while moving, clicking and dragging the mouse pointer over the drawing area. While the
selection of a tool has no immidiate effect on the drawn structure, pressing a button
does. Currently available buttons allow to clean up atom coordinates or to revert the
most recent structure change.</p>
<table BORDER=1 CELLSPACING=0 CELLPADDING=4 CLASS=body width="100%"> <tr align="Left">  <th>Button or Tool</th>  <th>Name</th>  <th>Explanation</th> </tr> <tr>
  <td><img src="atomTools.gif" width="48" height="152" border="0"></td>
  <td>Atom Tools</td>
  <td>The Atom Tools cover atoms frequently used in organic chemistry. Afterselecting one of these tools, you may place new atoms by clicking into theempty space or change existing atom by clicking onto them.</td> </tr> <tr>  <td><img src="otherAtomTool.gif" width="22" height="22" border="0"></td>  <td>Atom Detail Tool</td>  <td>Double clicking an atom with this tool selected will open a dialog window
for specifying an unusual atom label, specific isotop, abnormal valence
and/or radical state. When closing the dialog the double clicked atom is changed
accordingly. The dialog settings are remembered applied to any other clicked atom,
as long as the tool is selected.</td> </tr> <tr>  <td><img src="chargeTools.gif" width="48" height="22" border="0"></td>  <td>Charge Tools</td>  <td>These tools let you assign charges to atoms. Multiple clicks on thesame atom will increase or decrease the charge by 1. The <b>Osiris StructureEditor</b> assumes the presence of implicit hydrogens at any charged or noncharged atoms to meet the atom's default valence. However, implicit hydrogensare only shown on hetero atoms.</td> </tr> <tr>  <td><img src="ringTools.gif" width="48" height="74" border="0"></td>  <td>Ring Tools</td>
  <td>After selecting one of the predefined rings, one may create a new ring
or attach a ring to an existing bond or atom to create annelated ring systems
or a spiro compound, respectively.</td> </tr> <tr>  <td><img src="bondTools.gif" width="22" height="74" border="0"></td>  <td>Bond Tools</td>  <td>Bond Tools allow you to create new bonds and to change existing bondsconcerning their order or stereo-orientation. By clicking into the openspace you create a new bond of the selected type including two carbon atoms.
Clicking onto an existing atom will attach a new carbon. Dragging the mouse fromone atom to another one will just connect these atoms or increment the bond order
between them, if they were already connected. If the plain single bond tool is
selected, bonds may be multiply clicked to cycle through the possible bond orders.
Where reasonable, it also toggles between double bonds with known or unknown
configuration, the so-called cross bond.
When using stereo bonds please consider that the pointed tip of the bond should
always point to the stereo center.</td> </tr> <tr>  <td><img src="chainTool.gif" width="22" height="22" border="0"></td>  <td>Chain Tool</td>  <td>The Chain Tool provides the fastest way to draw aliphatic carbon chains in
zig-zag orientation. With the selected Chain Tool click into the empty space or at
an existing atom and drag the mouse to create a new zig-zag chain and flip its
orientation.</td> </tr> <tr>  <td><img src="esrTools.gif" width="22" height="74" border="0"></td>  <td>ESR Tools</td>  <td>The editor supports the enhanced stereo recognition (ESR) introduced by
Molecular Design Ltd. with IsisDraw V2.5. The ESR Tools allow to define for every
stereo center, whether it is an absolute one or if it belongs to a group of stereo
centers that have the drawn, but relative configuration. For any group of relative
stereo centers one may define that the drawn <b>and</b> the inverse configurations are present,
i.e. that we have a racemic situation concerning the group members. This is indicated by
green stereo bonds and an ampersand '<b>&</b>' at the stereo centers. Likewise one may
define groups of relative stereo centers that contain either the drawn configuration <b>or</b>
the opposite one. Stereo centers of such a group are indicated by blue stereo bonds and
the word '<b>or</b>' at the stereo centers. In addition to the '<b>&</b>' or '<b>or</b>'
indicators group numbers show which stereo centers belong to the same group.</td> </tr> <tr>  <td><img src="unknownConfigurationTool.gif" width="22" height="22" border="0"></td>   <td>Unknown Configuration Tool</td>   <td>This symbol is used to denote an unknown stereo configuration at a chiral center.</td> </tr> <tr>  <td><img src="cleanUpButton.gif" width="22" height="22" border="0"></td>  <td>Cleanup Button</td>  <td>A cleanup will generate new coordinates of an existing molecule. Itrearranges bond and atom positions in order to have a proper 2D structure.
If a part of the molecule or reaction is selected, the cleanup will retain
the relative orientation of the non-selected atoms.</td> </tr> <tr>  <td><img src="lassoPointerTool.gif" width="22" height="22" border="0"></td>  <td>Lasso Pointer Tool</td>  <td>This tools allows you to select multiple atoms and bonds to rearrange,
rotate, resize, delete or duplicate at the same time. Just drag the mouse pointer
around the atoms of interest. Selected atoms and bonds are shown in red. By pressing
the control key you switch to the rectangular selection mode and the shift key lets
you add atoms to the current selection. By clicking onto an atom or bonds and dragging
the mouse one may more it or all selected atoms, if the clicked one is selected.
When pressing the shift key while dragging a selected fragment, an automatically created
copy of the selected fragment is dragged.
Where the editor needs to support multiple molecules, e.g. if a reaction is edited,
then every reactant and product is indicated by a large light gray indicator in
the background ('A', 'B', 'P1', etc.). Where independent fragments shall be treated
as one molecule, e.g. anion and kation of one salt, one must locate those fragments
close enough that there is only one indicator behind them.
If a reaction or molecule query is edited, then one may double click an atom or
a set of selected atoms to open a query feature dialog to specify additional conditions
for a fragment to match in a substructure search. The same applies to individual or
multiple selected bonds. If the edited object is not a query then double clicking of
an atom or bond will just select the entire fragment.</td> </tr> <tr>  <td><img src="deleteTool.gif" width="22" height="22" border="0"></td>  <td>Delete Tool</td>  <td>It allows you to delete individual atoms or bonds or selected parts of the molecule.
Selected areas may also be removed by pressing the delete key from the keyboard.</td> </tr> <tr>  <td><img src="zoomAndRotateTool.gif" width="22" height="22" border="0"></td>  <td>Zoom and Rotate Tool</td>  <td>This tool allows to zoom or rotate the entire drawing or a selected subset.
Just click at the intended origin for the rotation or zooming and drag the mouse vertically
to zoom or horizontically to rotate.</td> </tr> <tr>  <td><img src="mappingTool.gif" width="22" height="22" border="0"></td>  <td>Mapping Tool</td>  <td>This tool is only available when a reaction is edited. Use this tool to
map reactant atoms to the respective product atoms. This is done by clicking on
a reactant atom and dragging the mouse onto the corresponding product atom. The
editor will acknowledge the link by displaying a red mapping number at both atoms.
Afterwards it tries to map atoms in the vicinity automatically and displays green
numbers at automatically mapped atoms. Please assign manually as many reactant-product
pairs as are needed that the entire reaction is mapped completely and correctly.
Pressing the 'Delete' key while this tool is selected removes all mapping from the reaction.</td> </tr> <tr>  <td><img src="textTool.gif" width="22" height="22" border="0"></td>  <td>Text Tool</td>  <td>The text tool may only be selected in certain situations. If it is selected
one may use it to place text elements directly into the drawing. These text elements
will be integral part of the drawing and, thus, move, resize and rotate with the molecules
or reaction.</td> </tr></table></body></html>
